The Sierra Leone defender, who joined the Terriers on loan from Chelsea in the summer, levelled for Jan Siewert’s men before Junior Hoilett notched the match-winner.
Joe Ralls opened the scoring in the 42nd minute before Chalobah drew his side level five minutes into the second half.
Hoilett then grabbed the winning goal in the 88th minute to deny Huddersfield a share of the points in their second away game of the season.
Chalobah featured for 77 minutes before making way for Juninho Bacuna while DR Congo’s Isaac Mbenza was replaced by Adama Diakhaby.
The defeat saw Huddersfield drop to 23rd place on the table after picking up one point from four games.
They will hope to bounce back from the setback in their next league game against Reading on Saturday.